Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 22 Mar 2016 12:05:59 +0100
Description: Since r-cran-geiger is not yet packaged we
 need to exclude the test that are requiring this package

--- a/tests/testthat/geiger_test.R
+++ /dev/null
@@ -1,56 +0,0 @@
-context("Geiger tests (may take 15+ minutes)")
-
-
-library(geiger)
-
-
-test_that("We can write caudata data to nexml", {
-  data(caudata)
-  nexml_write(trees = caudata$phy, characters = caudata$dat, file="tmp.xml")
-  expect_true_or_null(nexml_validate("tmp.xml"))
-  unlink("tmp.xml") # cleanup
-})
-
-
-test_that("We can write geospiza data to nexml", {
-  data(geospiza)
-  nexml_write(trees = geospiza$phy, characters = geospiza$dat, file="tmp.xml")
-  expect_true_or_null(nexml_validate("tmp.xml"))
-  unlink("tmp.xml") # cleanup
-})
-
-test_that("We can write chelonia data to nexml", {
-  data(chelonia)
-  nexml_write(trees = chelonia$phy, characters = chelonia$dat, file="tmp.xml")
-  expect_true_or_null(nexml_validate("tmp.xml"))
-  unlink("tmp.xml") # cleanup
-})
-
-test_that("We can write primates data to nexml", {
-  data(primates)
-  nexml_write(trees = primates$phy, characters = primates$dat, file="tmp.xml")
-  expect_true_or_null(nexml_validate("tmp.xml"))
-  unlink("tmp.xml") # cleanup
-})
-
-test_that("We can write whales data to nexml", {
-  data(whales)
-# taxa need to be rownames not separate column 
-  whales$dat <- whales$richness[[2]]
-  names(whales$dat) <- whales$richness[[1]] 
-  nexml_write(trees = whales$phy, characters = whales$dat, file="tmp.xml")
-  expect_true_or_null(nexml_validate("tmp.xml"))
-  unlink("tmp.xml") # cleanup
-})
-
-
-test_that("We can write amphibia multiphylo to nexml. Two of these phylogenies each have nearly 3K taxa, so this may take around 12 minutes", {
-# multiphylo, where two phylogenies have each nearly 3K taxa
-  data(amphibia)
-  class(amphibia) <- "multiPhylo"
-  runtime <- system.time(nexml_write(amphibia, file="tmp.xml")) # Slow! about 12 minutes
-
-  expect_true_or_null(nexml_validate("tmp.xml"))
-  unlink("tmp.xml") # cleanup
-})
-
--- a/tests/testthat/test_comp_analysis.R
+++ /dev/null
@@ -1,29 +0,0 @@
-context("Comparative analysis")
-
-
-library(geiger)
-
-
-test_that("We can extract tree and trait data to run fitContinuous and fitDiscrete", {
-  nexml <- read.nexml(system.file("examples", "comp_analysis.xml", package="RNeXML"))
-  traits <- get_characters(nexml)
-  tree <- get_trees(nexml)
-  expect_is(tree, "phylo")
-  cts <- fitContinuous(tree, traits[1], ncores=1)
-  ## Incredibly, fitDiscrete cannot take discrete characters
-  # dte <- fitDiscrete(tree, traits[2], ncores=1)
-  traits[[2]] <- as.numeric(traits[[2]])
-  dte <- fitDiscrete(tree, traits[2], ncores=1)
-  
-})
-
-
-test_that("We can serialize tree and trait data for a comparative analysis", {
-  data(geospiza)
-  add_trees(geospiza$phy)
-  nexml <- add_characters(geospiza$dat)
-  write.nexml(nexml, file = "geospiza.xml")
-  expect_true_or_null(nexml_validate("geospiza.xml"))
-  unlink("geospiza.xml")
-})
-
--- a/tests/testthat/test_characters.R
+++ b/tests/testthat/test_characters.R
@@ -101,13 +101,3 @@ test_that("we can add characters to a ne
 
 
 
-## based on bug on 2014-03-12 65ae459523c529452adb699c3d5d118c0a207402 
-test_that("we can add multiple character matrices to a nexml file", {
-          library("geiger")
-          data(geospiza)
-          data(primates)
-          nex <- add_characters(geospiza$dat)
-          nex <- add_characters(primates$dat, nex)
-          expect_is(nex, "nexml")
-})
-